{"id":"https://openalex.org/W4414648166","doi":"https://doi.org/10.1109/cibcb66090.2025.11177078","title":"Self-Attention Enhanced Deep Learning Models for Immune Cell Deconvolution from Bulk RNA-Seq","display_name":"Self-Attention Enhanced Deep Learning Models for Immune Cell Deconvolution from Bulk RNA-Seq","publication_year":2025,"publication_date":"2025-08-20","ids":{"openalex":"https://openalex.org/W4414648166","doi":"https://doi.org/10.1109/cibcb66090.2025.11177078"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb66090.2025.11177078","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb66090.2025.11177078","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067453693","display_name":"Chia\u2010Ru Chung","orcid":"https://orcid.org/0000-0002-4548-7620"},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chia-Ru Chung","raw_affiliation_strings":["National Central University,Department of Computer Science and Information Engineering,Taoyuan City,Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Central University,Department of Computer Science and Information Engineering,Taoyuan City,Taiwan","institution_ids":["https://openalex.org/I22265921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100670010","display_name":"Yen\u2010Lin Chen","orcid":"https://orcid.org/0000-0001-7717-9393"},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yen-Lin Chen","raw_affiliation_strings":["National Central University,Department of Computer Science and Information Engineering,Taoyuan City,Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Central University,Department of Computer Science and Information Engineering,Taoyuan City,Taiwan","institution_ids":["https://openalex.org/I22265921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101714041","display_name":"Yun Tang","orcid":"https://orcid.org/0000-0002-8807-5239"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yun Tang","raw_affiliation_strings":["National Yang Ming Chiao Tung University,Institute of Bioinformatics and Systems Biology,Hsinchu City,Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Yang Ming Chiao Tung University,Institute of Bioinformatics and Systems Biology,Hsinchu City,Taiwan","institution_ids":["https://openalex.org/I148366613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013309172","display_name":"Justin Bo\u2010Kai Hsu","orcid":null},"institutions":[{"id":"https://openalex.org/I99908691","display_name":"Yuan Ze University","ror":"https://ror.org/01fv1ds98","country_code":"TW","type":"education","lineage":["https://openalex.org/I99908691"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Justin Bo-Kai Hsu","raw_affiliation_strings":["Yuan Ze University,Department of Computer Science and Engineering,Taoyuan City,Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yuan Ze University,Department of Computer Science and Engineering,Taoyuan City,Taiwan","institution_ids":["https://openalex.org/I99908691"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111961302","display_name":"Li-Ching Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Li-Ching Wu","raw_affiliation_strings":["National Central University,Department of Biomedical Sciences and Engineering,Taoyuan City,Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Central University,Department of Biomedical Sciences and Engineering,Taoyuan City,Taiwan","institution_ids":["https://openalex.org/I22265921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045675277","display_name":"Tzong-Yi Lee","orcid":"https://orcid.org/0000-0001-8475-7868"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Tzong-Yi Lee","raw_affiliation_strings":["National Yang Ming Chiao Tung University,Institute of Bioinformatics and Systems Biology,Hsinchu City,Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Yang Ming Chiao Tung University,Institute of Bioinformatics and Systems Biology,Hsinchu City,Taiwan","institution_ids":["https://openalex.org/I148366613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016211165","display_name":"Jorng\u2010Tzong Horng","orcid":"https://orcid.org/0000-0002-7671-0573"},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jorng-Tzong Horng","raw_affiliation_strings":["National Central University,Department of Computer Science and Information Engineering,Taoyuan City,Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Central University,Department of Computer Science and Information Engineering,Taoyuan City,Taiwan","institution_ids":["https://openalex.org/I22265921"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11316","display_name":"Mycobacterium research and diagnosis","score":0.9775999784469604,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11316","display_name":"Mycobacterium research and diagnosis","score":0.9775999784469604,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9488999843597412,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9463000297546387,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/deconvolution","display_name":"Deconvolution","score":0.798799991607666},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.7440999746322632},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.44830000400543213},{"id":"https://openalex.org/keywords/generalizability-theory","display_name":"Generalizability theory","score":0.44769999384880066},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.43320000171661377},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.42649999260902405},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.36320000886917114},{"id":"https://openalex.org/keywords/cell-type","display_name":"Cell type","score":0.3465000092983246}],"concepts":[{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.798799991607666},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.7440999746322632},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6509000062942505},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6266999840736389},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5288000106811523},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.44830000400543213},{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.44769999384880066},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.43320000171661377},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.42649999260902405},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4142000079154968},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.36320000886917114},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.3465000092983246},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3285999894142151},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.3158999979496002},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3084999918937683},{"id":"https://openalex.org/C2780575108","wikidata":"https://www.wikidata.org/wiki/Q7316652","display_name":"Retargeting","level":2,"score":0.30399999022483826},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.2906000018119812},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.2888000011444092},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.2865999937057495},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2791000008583069},{"id":"https://openalex.org/C145741570","wikidata":"https://www.wikidata.org/wiki/Q7251534","display_name":"Proteogenomics","level":5,"score":0.2766999900341034},{"id":"https://openalex.org/C137061746","wikidata":"https://www.wikidata.org/wiki/Q736033","display_name":"Peripheral blood mononuclear cell","level":3,"score":0.2754000127315521},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.2745000123977661},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.258899986743927},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.25679999589920044},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2524999976158142}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb66090.2025.11177078","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb66090.2025.11177078","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320308611","display_name":"Health Research","ror":"https://ror.org/059qgvg50"},{"id":"https://openalex.org/F4320311687","display_name":"Ministry of Education","ror":"https://ror.org/03m01yf64"},{"id":"https://openalex.org/F4320331164","display_name":"National Science and Technology Council","ror":"https://ror.org/00wnb9798"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1985987855","https://openalex.org/W2008161400","https://openalex.org/W2048877126","https://openalex.org/W2060427373","https://openalex.org/W2134342374","https://openalex.org/W2148226248","https://openalex.org/W2297219066","https://openalex.org/W2313339984","https://openalex.org/W2479362027","https://openalex.org/W2794480084","https://openalex.org/W2884964182","https://openalex.org/W2907514116","https://openalex.org/W2911922390","https://openalex.org/W2913970879","https://openalex.org/W2921330004","https://openalex.org/W2942610007","https://openalex.org/W2952240309","https://openalex.org/W2953866345","https://openalex.org/W2967035454","https://openalex.org/W2981732942","https://openalex.org/W2995410603","https://openalex.org/W3019556496","https://openalex.org/W3044352330","https://openalex.org/W3112908745","https://openalex.org/W3186021169","https://openalex.org/W4200135473","https://openalex.org/W4221065117","https://openalex.org/W4224470052","https://openalex.org/W4308589388","https://openalex.org/W4385245566"],"related_works":[],"abstract_inverted_index":{"Accurate":[0],"immune":[1,53,63],"cell":[2,54,64,74,112,164],"composition":[3,102],"profiling":[4],"is":[5,19,178],"crucial":[6],"for":[7,51,110,162,214],"understanding":[8],"immunological":[9],"dynamics":[10],"and":[11,26,77,130,136,190,200,217],"disease":[12],"mechanisms.":[13],"Bulk":[14],"RNA":[15],"sequencing":[16],"(bulk":[17],"RNA-seq)":[18],"widely":[20],"employed":[21],"due":[22,180],"to":[23,33,149,181,206],"its":[24],"cost-effectiveness":[25],"scalability;":[27],"however,":[28],"it":[29],"lacks":[30],"the":[31,106,147,195],"resolution":[32],"identify":[34],"cell-specific":[35],"gene":[36,155],"expression.":[37],"To":[38],"address":[39],"this":[40],"limitation,":[41],"we":[42,93,173],"propose":[43],"a":[44],"self-attention":[45,119,145,198],"enhanced":[46,120],"deep":[47,121],"learning":[48,122],"model":[49,123,148],"designed":[50],"precise":[52],"deconvolution":[55,160,209],"from":[56,66],"bulk":[57],"RNA-seq":[58,69,97],"data.":[59],"We":[60],"systematically":[61],"annotated":[62],"types":[65,189],"four":[67],"single-cell":[68],"(scRNA-seq)":[70],"peripheral":[71],"blood":[72],"mononuclear":[73],"(PBMC)":[75],"datasets":[76],"validated":[78],"these":[79,91],"annotations":[80],"against":[81],"established":[82],"automated":[83],"identification":[84],"tools":[85,213],"(SingleR,":[86],"Seurat,":[87],"scPred,":[88],"ScType).":[89],"Leveraging":[90],"annotations,":[92],"generated":[94],"realistic":[95,201],"pseudo-bulk":[96],"training":[98,202],"samples":[99],"using":[100],"Dirichlet-distribution-based":[101],"sampling,":[103],"significantly":[104],"enhancing":[105],"model\u2019s":[107],"performance,":[108],"particularly":[109],"rare":[111],"populations.":[113],"Comparative":[114],"evaluations":[115],"demonstrated":[116],"that":[117,175],"our":[118],"consistently":[124],"outperformed":[125],"existing":[126],"approaches,":[127],"including":[128],"CIBERSORTx":[129],"Scaden,":[131],"achieving":[132],"lower":[133],"prediction":[134],"errors":[135],"higher":[137],"correlations":[138],"on":[139,170],"benchmark":[140],"PBMC":[141,171],"datasets.":[142],"Integrating":[143],"multi-head":[144],"allowed":[146],"dynamically":[150],"capture":[151],"intricate":[152],"dependencies":[153],"among":[154],"expression":[156],"features,":[157],"substantially":[158],"improving":[159],"accuracy":[161],"specific":[163],"subsets.":[165],"While":[166],"demonstrating":[167],"robust":[168],"performance":[169],"datasets,":[172],"acknowledge":[174],"broader":[176],"validation":[177],"essential":[179],"potential":[182,196],"limitations":[183],"in":[184],"generalizability":[185],"across":[186],"different":[187],"tissue":[188],"conditions.":[191],"Our":[192],"study":[193],"highlights":[194],"of":[197],"mechanisms":[199],"data":[203],"generation":[204],"strategies":[205],"enhance":[207],"computational":[208],"techniques,":[210],"providing":[211],"valuable":[212],"clinical":[215],"diagnostics":[216],"translational":[218],"immunology":[219],"research.":[220]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
